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Abstract
A wide range of biomaterials and engineered cell surfaces are composed of bioconjugates embedded in liposome membranes, surface-immobilized bilayers, or the plasma membranes of living cells. This review article summarizes the various ways that Nature anchors integral and peripheral proteins in a cell membrane and describes the strategies devised by chemical biologists to label a membrane protein in living cells. Also discussed are modern synthetic and semisynthetic methods to produce lipidated proteins. Subsequent sections describe methods to anchor a three-component synthetic construct that is composed of a lipophilic membrane anchor, hydrophilic linker, and exposed functional component. The surface exposed payload can be a fluorophore, aptamer, oligonucleotide, polypeptide, peptide nucleic acid, polysaccharide, branched dendrimer, or linear polymer. Hydrocarbon chains are commonly used as the membrane anchor, and a general experimental trend is that a two chain lipid anchor has higher membrane affinity than a cholesteryl or single chain lipid anchor. Amphiphilic fluorescent dyes are effective molecular probes for cell membrane imaging and a zwitterionic linker between the fluorophore and the lipid anchor promotes high persistence in the plasma membrane of living cells. A relatively new advance is the development of switchable membrane anchors as molecular tools for fundamental studies or as technology platforms for applied biomaterials.
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Affiliation(s)
- Rananjaya S Gamage
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jordan L Chasteen
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Bradley D Smith
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556, United States
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2
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Maity S, Bingham C, Sheng W, Ehyaei N, Chakraborty D, Tahmasebi-Nick S, Kimmel TE, Vasileiou C, Geiger JH, Borhan B. Light controlled reversible Michael addition of cysteine: a new tool for dynamic site-specific labeling of proteins. Analyst 2023; 148:1085-1092. [PMID: 36722993 PMCID: PMC9992065 DOI: 10.1039/d2an01395a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Cysteine-based Michael addition is a widely employed strategy for covalent conjugation of proteins, peptides, and drugs. The covalent reaction is irreversible in most cases, leading to a lack of control over the process. Utilizing spectroscopic analyses along with X-ray crystallographic studies, we demonstrate Michael addition of an engineered cysteine residue in human Cellular Retinol Binding Protein II (hCRBPII) with a coumarin analog that creates a non-fluorescent complex. UV-illumination reverses the conjugation, yielding a fluorescent species, presumably through a retro-Michael process. This series of events can be repeated between a bound and non-bound form of the cysteine reversibly, resulting in the ON-OFF control of fluorescence. The details of the mechanism of photoswitching was illuminated by recapitulation of the process in light irradiated single crystals, confirming the mechanism at atomic resolution.
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Affiliation(s)
- Soham Maity
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA.
| | - Courtney Bingham
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA.
| | - Wei Sheng
- Roche Tissue Diagnostics, 1910 E Innovation Park Dr, Oro Valley, AZ, 85755, USA
| | - Nona Ehyaei
- Lycia Therapeutics, 400 East Jamie Court, S San Francisco, CA 94080, USA
| | - Debarshi Chakraborty
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA.
| | | | - Thomas E Kimmel
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA.
| | - Chrysoula Vasileiou
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA.
| | - James H Geiger
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA.
| | - Babak Borhan
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln., East Lansing, MI 48824, USA.
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3
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Zuo J, Zhu E, Yin W, Yao C, Liao J, Ping X, Zhu Y, Cai X, Rao Y, Feng H, Zhang K, Qian Z. Long-term spatiotemporal and highly specific imaging of the plasma membrane of diverse plant cells using a near-infrared AIE probe. Chem Sci 2023; 14:2139-2148. [PMID: 36845931 PMCID: PMC9945320 DOI: 10.1039/d2sc05727a] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/19/2023] [Indexed: 01/21/2023] Open
Abstract
Fluorescent probes are valuable tools to visualize plasma membranes intuitively and clearly and their related physiological processes in a spatiotemporal manner. However, most existing probes have only realized the specific staining of the plasma membranes of animal/human cells within a very short time period, while almost no fluorescent probes have been developed for the long-term imaging of the plasma membranes of plant cells. Herein, we designed an AIE-active probe with NIR emission to achieve four-dimensional spatiotemporal imaging of the plasma membranes of plant cells based on a collaboration approach involving multiple strategies, demonstrated long-term real-time monitoring of morphological changes of plasma membranes for the first time, and further proved its wide applicability to plant cells of different types and diverse plant species. In the design concept, three effective strategies including the similarity and intermiscibility principle, antipermeability strategy and strong electrostatic interactions were combined to allow the probe to specifically target and anchor the plasma membrane for an ultralong amount of time on the premise of guaranteeing its sufficiently high aqueous solubility. The designed APMem-1 can quickly penetrate cell walls to specifically stain the plasma membranes of all plant cells in a very short time with advanced features (ultrafast staining, wash-free, and desirable biocompatibility) and the probe shows excellent plasma membrane specificity without staining other areas of the cell in comparison to commercial FM dyes. The longest imaging time of APMem-1 can be up to 10 h with comparable performance in both imaging contrast and imaging integrity. The validation experiments on different types of plant cells and diverse plants convincingly proved the universality of APMem-1. The development of plasma membrane probes with four-dimensional spatial and ultralong-term imaging ability provides a valuable tool to monitor the dynamic processes of plasma membrane-related events in an intuitive and real-time manner.
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Affiliation(s)
- Jiaqi Zuo
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Material Sciences, Zhejiang Normal University Yingbin Road 688 Jinhua 321004 China
| | - Engao Zhu
- College of Life Sciences, Zhejiang Normal University Yingbin Road 688 Jinhua 321004 China
| | - Wenjing Yin
- College of Life Sciences, Zhejiang Normal University Yingbin Road 688 Jinhua 321004 China
| | - Chuangye Yao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Material Sciences, Zhejiang Normal University Yingbin Road 688 Jinhua 321004 China
| | - Jiajia Liao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Material Sciences, Zhejiang Normal University Yingbin Road 688 Jinhua 321004 China
| | - Xinni Ping
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Material Sciences, Zhejiang Normal University Yingbin Road 688 Jinhua 321004 China
| | - Yuqing Zhu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Material Sciences, Zhejiang Normal University Yingbin Road 688 Jinhua 321004 China
| | - Xuting Cai
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Material Sciences, Zhejiang Normal University Yingbin Road 688 Jinhua 321004 China
| | - Yuchun Rao
- College of Life Sciences, Zhejiang Normal University Yingbin Road 688 Jinhua 321004 China
| | - Hui Feng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Material Sciences, Zhejiang Normal University Yingbin Road 688 Jinhua 321004 China
| | - Kewei Zhang
- College of Life Sciences, Zhejiang Normal University Yingbin Road 688 Jinhua 321004 China
| | - Zhaosheng Qian
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Material Sciences, Zhejiang Normal University Yingbin Road 688 Jinhua 321004 China
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Ray DM, Flood JR, David Y. Harnessing Split-Inteins as a Tool for the Selective Modification of Surface Receptors in Live Cells. Chembiochem 2023; 24:e202200487. [PMID: 36178424 PMCID: PMC9977608 DOI: 10.1002/cbic.202200487] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/29/2022] [Indexed: 02/04/2023]
Abstract
Biochemical studies of integral membrane proteins are often hampered by low purification yields and technical limitations such as aggregation causing in vitro manipulations to be challenging. The ability of controlling proteins in live cells bypasses these limitations while broadening the scope of accessible questions owing to the proteins being in their native environment. Here we take advantage of the intein biorthogonality to mammalian systems, site specificity, fast kinetics, and auto-processing nature as an attractive option for modifying surface proteins. Using EGFR as a model, we demonstrate that the split-intein pair AvaN /NpuC can be used to efficiently and specifically modify target membrane proteins with a synthetic adduct for downstream live cell application.
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Affiliation(s)
- Devin M Ray
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, 10065, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Julia R Flood
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yael David
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, 10065, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY, 10065, USA
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5
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Roy S, Curry SD, Bagot CC, Mueller EN, Mansouri AM, Park W, Cha JN, Goodwin AP. Enzyme Prodrug Therapy with Photo-Cross-Linkable Anti-EGFR Affibodies Conjugated to Upconverting Nanoparticles. ACS NANO 2022; 16:15873-15883. [PMID: 36129781 PMCID: PMC10197967 DOI: 10.1021/acsnano.2c02558] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In this work, we demonstrate that a photo-cross-linkable conjugate of upconverting nanoparticles and cytosine deaminase can catalyze prodrug conversion specifically at tumor sites in vivo. Non-covalent association of proteins and peptides with cellular surfaces leads to receptor-mediated endocytosis and catabolic degradation. Recently, we showed that covalent attachment of proteins such as affibodies to cell receptors yields extended expression on cell surfaces with preservation of protein function. To adapt this technology for in vivo applications, conjugates were prepared from upconverting nanoparticles and fusion proteins of affibody and cytosine deaminase enzyme (UC-ACD). The affibody allows covalent photo-cross-linking to epidermal growth factor receptors (EGFRs) overexpressed on Caco-2 human colorectal cancer cells under near-infrared (NIR) light. Once bound, the cytosine deaminase portion of the fusion protein converts the prodrug 5-fluorocytosine (5-FC) to the anticancer drug 5-fluorouracil (5-FU). NIR covalent photoconjugation of UC-ACD to Caco-2 cells showed 4-fold higher retention than observed with cells that were not irradiated in vitro. Next, athymic mice expressing Caco-2 tumors showed 5-fold greater UC-ACD accumulation in the tumors than either conjugates without the CD enzyme or UC-ACDs in the absence of NIR excitation. With oral administration of 5-FC prodrug, tumors with photoconjugated UC-ACD yielded 2-fold slower growth than control groups, and median mouse survival increased from 28 days to 35 days. These experiments demonstrate that enzyme-decorated nanoparticles can remain viable after a single covalent photoconjugation in vivo, which can in turn localize prodrug conversion to tumor sites for multiple weeks.
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Affiliation(s)
- Shambojit Roy
- Department of Chemical and Biological Engineering, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
| | - Shane D. Curry
- Department of Chemical and Biological Engineering, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
| | - Conrad Corbella Bagot
- Department of Electrical, Computer, and Energy Engineering, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
| | - Evan N. Mueller
- Department of Chemical and Biological Engineering, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
| | - Abdulrahman M. Mansouri
- Department of Chemical and Biological Engineering, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
| | - Wounjhang Park
- Department of Electrical, Computer, and Energy Engineering, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
| | - Jennifer N. Cha
- Department of Chemical and Biological Engineering, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
- Materials Science and Engineering Program, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
| | - Andrew P. Goodwin
- Department of Chemical and Biological Engineering, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
- Materials Science and Engineering Program, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
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Matsuzaki K. Elucidation of Complex Dynamic Intermolecular Interactions in Membranes. Chem Pharm Bull (Tokyo) 2022; 70:1-9. [PMID: 34980725 DOI: 10.1248/cpb.c21-00815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Biomembranes composed of various proteins and lipids play important roles in cellular functions, such as signal transduction and substance transport. In addition, some bioactive peptides and pathogenic proteins target membrane proteins and lipids to exert their effects. Therefore, an understanding of dynamic and complex intermolecular interactions among these membrane constituents is needed to elucidate their mechanisms. This review summarizes the major research carried out in the author's laboratory on how lipids and their inhomogeneous distributions regulate the structures and functions of antimicrobial peptides and Alzheimer's amyloid β-protein. Also, how to detect transmembrane helix-helix and membrane protein-protein interactions and how they are modulated by lipids are discussed.
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Ntostis P, Iles D, Kokkali G, Vaxevanoglou T, Kanavakis E, Pantou A, Huntriss J, Pantos K, Picton HM. The impact of maternal age on gene expression during the GV to MII transition in euploid human oocytes. Hum Reprod 2021; 37:80-92. [PMID: 34755188 PMCID: PMC8730309 DOI: 10.1093/humrep/deab226] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 09/18/2021] [Indexed: 12/27/2022] Open
Abstract
STUDY QUESTION Are there age-related differences in gene expression during the germinal vesicle (GV) to metaphase II (MII) stage transition in euploid human oocytes? SUMMARY ANSWER A decrease in mitochondrial-related transcripts from GV to MII oocytes was observed, with a much greater reduction in MII oocytes with advanced age. WHAT IS KNOWN ALREADY Early embryonic development is dependent on maternal transcripts accumulated and stored within the oocyte during oogenesis. Transcriptional activity of the oocyte, which dictates its ultimate developmental potential, may be influenced by age and explain the reduced competence of advanced maternal age (AMA) oocytes compared with the young maternal age (YMA). Gene expression has been studied in human and animal oocytes; however, RNA sequencing could provide further insights into the transcriptome profiling of GV and in vivo matured MII euploid oocytes of YMA and AMA patients. STUDY DESIGN, SIZE, DURATION Fifteen women treated for infertility in a single IVF unit agreed to participate in this study. Five GV and 5 MII oocytes from 6, 21-26 years old women (YMA cohort) and 5 GV and 6 MII oocytes from 6, 41-44 years old women (AMA cohort) undergoing IVF treatment were donated. The samples were collected within a time frame of 4 months. RNA was isolated and deep sequenced at the single-cell level. All donors provided either GV or MII oocytes. PARTICIPANTS/MATERIALS, SETTING, METHODS Cumulus dissection from donated oocytes was performed 38 h after hCG injection, denuded oocytes were inserted into lysis buffer supplemented with RNase inhibitor. The samples were stored at -80°C until further use. Isolated RNA from GV and MII oocytes underwent library preparation using an oligo deoxy-thymidine (dT) priming approach (SMART-Seq v4 Ultra Low Input RNA assay; Takara Bio, Japan) and Nextera XT DNA library preparation assay (Illumina, USA) followed by deep sequencing. Data processing, quality assessment and bioinformatics analysis were performed using source-software, mainly including FastQC, HISAT2, StringTie and edgeR, along with functional annotation analysis, while scploid R package was employed to determine the ploidy status. MAIN RESULTS AND THE ROLE OF CHANCE Following deep sequencing of single GV and MII oocytes in both YMA and AMA cohorts, several hundred transcripts were found to be expressed at significantly different levels. When YMA and AMA MII oocyte transcriptomes were compared, the most significant of these were related to mitochondrial structure and function, including biological processes, mitochondrial respiratory chain complex I assembly and mitochondrial translational termination (false discovery rate (FDR) 6.0E-10 to 1.2E-7). These results indicate a higher energy potential of the YMA MII cohort that is reduced with ageing. Other biological processes that were significantly higher in the YMA MII cohort included transcripts involved in the translation process (FDR 1.9E-2). Lack of these transcripts could lead to inappropriate protein synthesis prior to or upon fertilisation of the AMA MII oocytes. LARGE SCALE DATA The RNA sequencing data were deposited in the Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo), under the accession number: GSE164371. LIMITATIONS, REASONS FOR CAUTION The relatively small sample size could be a reason for caution. However, the RNA sequencing results showed homogeneous clustering with low intra-group variation and five to six biological replicates derived from at least three different women per group minimised the potential impact of the sample size. WIDER IMPLICATIONS OF THE FINDINGS Understanding the effects of ageing on the oocyte transcriptome could highlight the mechanisms involved in GV to MII transition and identify biomarkers that characterise good MII oocyte quality. This knowledge has the potential to guide IVF regimes for AMA patients. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by the Medical Research Council (MRC Grant number MR/K020501/1).
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Affiliation(s)
- P Ntostis
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - D Iles
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - G Kokkali
- Genesis Athens Clinic, Reproductive Medicine Unit, Athens, Greece
| | - T Vaxevanoglou
- Genesis Athens Clinic, Reproductive Medicine Unit, Athens, Greece
| | - E Kanavakis
- Genesis Athens Clinic, Reproductive Medicine Unit, Athens, Greece
| | - A Pantou
- Genesis Athens Clinic, Reproductive Medicine Unit, Athens, Greece
| | - J Huntriss
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - K Pantos
- Genesis Athens Clinic, Reproductive Medicine Unit, Athens, Greece
| | - H M Picton
- Genesis Genoma Laboratory, Athens, Greece
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Scheffer LK, Meinertzhagen IA. A connectome is not enough - what is still needed to understand the brain of Drosophila? J Exp Biol 2021; 224:272599. [PMID: 34695211 DOI: 10.1242/jeb.242740] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Understanding the structure and operation of any nervous system has been a subject of research for well over a century. A near-term opportunity in this quest is to understand the brain of a model species, the fruit fly Drosophila melanogaster. This is an enticing target given its relatively small size (roughly 200,000 neurons), coupled with the behavioral richness that this brain supports, and the wide variety of techniques now available to study both brain and behavior. It is clear that within a few years we will possess a connectome for D. melanogaster: an electron-microscopy-level description of all neurons and their chemical synaptic connections. Given what we will soon have, what we already know and the research that is currently underway, what more do we need to know to enable us to understand the fly's brain? Here, we itemize the data we will need to obtain, collate and organize in order to build an integrated model of the brain of D. melanogaster.
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Affiliation(s)
- Louis K Scheffer
- Howard Hughes Medical Institute, 19741 Smith Circle, Ashburn, VA 20147, USA
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Ma DL, Wu C, Liu H, Wu KJ, Leung CH. Luminescence approaches for the rapid detection of disease-related receptor proteins using transition metal-based probes. J Mater Chem B 2021; 8:3249-3260. [PMID: 31647090 DOI: 10.1039/c9tb01889a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Protein biomarkers, particularly abnormally expressed receptor proteins, have been proved to be one of the crucial biomarkers for the rapid assessment, diagnosis, prognosis and prediction of specific human diseases. Transition metal based strategies in particular possess delightful strengths in the in-field and real-time visualization of receptor proteins owing to their unique photophysical properties. In this review, we highlight recent advances in the development of detection methods for receptor protein biomarkers using transition metal based approaches, particularly those employing transition metal complexes. We first discuss the strengths and weaknesses of various strategies used for protein biomarker monitoring in live cells. We then describe the principles of the various sensing platforms and their application for receptor protein detection. Finally, we discuss the challenges and future inspirations in this specific field.
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Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry, Faculty of Science, Hong Kong Baptist University, Kowloon, Hong Kong SAR 999077, China.
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Thomas D, Rubio V, Iragavarapu V, Guzman E, Pelletier OB, Alamgir S, Zhang Q, Stawikowski MJ. Solvatochromic and pH-Sensitive Fluorescent Membrane Probes for Imaging of Live Cells. ACS Chem Neurosci 2021; 12:719-734. [PMID: 33508202 DOI: 10.1021/acschemneuro.0c00732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Membrane trafficking is essential for all cells, and visualizing it is particularly useful for studying neuronal functions. Here we report the synthesis, characterization, and application of several membrane- and pH-sensitive probes suitable for live-cell fluorescence imaging. These probes are based on a 1,8-naphthalimide fluorophore scaffold. They exhibit a solvatochromic effect, and one of them, ND6, shows a substantial fluorescence difference between pH 6 and 7. The solvatochromic effect and pH-sensitivity of those probes are explained using quantum chemical calculations, and molecular dynamics simulation confirms their integration and interaction with membrane lipids. For live-cell fluorescence imaging, we tested those probes in a cancer cell line (MCF7), cancer spheroids (MDA-MB-468), and cultured hippocampal neurons. Confocal imaging showed an excellent signal-to-noise ratio from 400:1 to about 1300:1 for cell membrane labeling. We applied ND6 during stimulation to label nerve terminals via dye uptake during evoked synaptic vesicle turnover. By ND6 imaging, we revealed cholesterol's multifaced role in replenishing synaptic vesicle pools. Our results demonstrate these fluorescent probes' great potential in studying membrane dynamic and synaptic functions in neurons and other secretory cells and tissues.
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Affiliation(s)
- Deborah Thomas
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida, United States
| | - Vicente Rubio
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida, United States
| | - Vijaya Iragavarapu
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida, United States
| | - Esther Guzman
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States
| | - Oliver B. Pelletier
- Department of Biomedical Sciences, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida, United States
| | - Shahriar Alamgir
- Department of Biomedical Sciences, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida, United States
- The Brain Institute, Florida Atlantic University, 5353 Parkside Drive, Jupiter, Florida, United States
| | - Qi Zhang
- Department of Biomedical Sciences, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida, United States
- The Brain Institute, Florida Atlantic University, 5353 Parkside Drive, Jupiter, Florida, United States
| | - Maciej J. Stawikowski
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida, United States
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Antenucci F, Ovsepian A, Wrobel A, Winther-Larsen HC, Bojesen AM. Design and Characterization of a Novel Tool for the Antigenic Enrichment of Actinobacillus pleuropneumoniae Outer Membrane. Pathogens 2020; 9:E1014. [PMID: 33276526 PMCID: PMC7761619 DOI: 10.3390/pathogens9121014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 11/30/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023] Open
Abstract
Production and isolation of recombinant proteins are costly and work-intensive processes, especially in immunology when tens or hundreds of potential immunogens need to be purified for testing. Here we propose an alternative method for fast screening of immunogen candidates, based on genetic engineering of recombinant bacterial strains able to express and expose selected antigens on their outer membrane. In Actinobacillus pleuropneumoniae, a Gram-negative porcine pathogen responsible for extensive economic losses worldwide, we identified a conserved general secretion pathway (GSP) domain in the N-terminal part of the outer membrane protein ApfA (ApfA stem: ApfAs). ApfAs was used as an outer membrane anchor, to which potential immunogens can be attached. To enable confirmation of correct positioning, ApfAs, was cloned in combination with the modified acyl carrier protein (ACP) fluorescent tag ACP mini (ACPm) and the putative immunogen VacJ. The chimeric construct was inserted in the pMK-express vector, subsequently transformed into A. pleuropneumoniae for expression. Flow cytometry, fluorescence imaging and mass spectrometry analysis were employed to demonstrate that the outer membrane of the transformed strain was enriched with the chimeric ApfAs-ACPm-VacJ antigen. Our results confirmed correct positioning of the chimeric ApfAs-ACPm-VacJ antigen and supported this system's potential as platform technology enabling antigenic enrichment of the outer membrane of A. pleuropneumoniae.
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Affiliation(s)
- Fabio Antenucci
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Copenhagen, Denmark; (F.A.); (A.O.)
| | - Armen Ovsepian
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Copenhagen, Denmark; (F.A.); (A.O.)
| | - Agnieszka Wrobel
- Section of Pharmaceutical Biosciences, Centre of Integrative Microbial Evolution, Department of Pharmacy, University of Oslo, Sem Sælandsvei 3, 0316 Oslo, Norway; (A.W.); (H.C.W.-L.)
| | - Hanne Cecilie Winther-Larsen
- Section of Pharmaceutical Biosciences, Centre of Integrative Microbial Evolution, Department of Pharmacy, University of Oslo, Sem Sælandsvei 3, 0316 Oslo, Norway; (A.W.); (H.C.W.-L.)
| | - Anders Miki Bojesen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Copenhagen, Denmark; (F.A.); (A.O.)
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12
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Roy S, Cha JN, Goodwin AP. Nongenetic Bioconjugation Strategies for Modifying Cell Membranes and Membrane Proteins: A Review. Bioconjug Chem 2020; 31:2465-2475. [PMID: 33146010 DOI: 10.1021/acs.bioconjchem.0c00529] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The cell membrane possesses an extensive library of proteins, carbohydrates, and lipids that control a significant portion of inter- and intracellular functions, including signaling, proliferation, migration, and adhesion, among others. Augmenting the cell surface composition would open possibilities for advances in therapy, tissue engineering, and probing fundamental cell processes. While genetic engineering has proven effective for many in vitro applications, these techniques result in irreversible changes to cells and are difficult to apply in vivo. Another approach is to instead attach exogenous functional groups to the cell membrane without changing the genetic nature of the cell. This review focuses on more recent approaches of nongenetic methods of cell surface modification through metabolic pathways, anchorage by hydrophobic interactions, and chemical conjugation. Benefits and drawbacks of each approach are considered, followed by a discussion of potential applications for nongenetic cell surface modification and an outlook on the future of the field.
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Stüber JC, Plückthun A. Labeling surface proteins with high specificity: Intrinsic limitations of phosphopantetheinyl transferase systems. PLoS One 2019; 14:e0226579. [PMID: 31856184 PMCID: PMC6922365 DOI: 10.1371/journal.pone.0226579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/28/2019] [Indexed: 12/04/2022] Open
Abstract
Objective Fluorescent labeling of specific cell-surface proteins enables a manifold of techniques to study their function in health and disease. A frequently cited family of methods employs phosphopantetheinyl transferases (PPTases) to attach probes, provided as conjugates of Coenzyme A. This method appears attractive, as only short peptide tags genetically fused to the protein of interest are needed as conjugation sites. Here, we describe observations we made when evaluating such protocols for delicate single-molecule applications where we require a particular combination of dyes, low background binding or low labeling of other proteins, and a high degree of labeling. Results When we tested a PPTase-acceptor peptide couple with several experimental protocols and various CoA conjugates for labeling of a protein on the cell surface, we noticed substantial non-specific labeling. For the first time, we provide here a quantification of the non-specific fraction of the signals obtained using appropriate controls. We further present evidence that this background is due to CoA-dye conjugates entering the cell, where they may be covalently attached to endogenous proteins. However, when studying cell-surface proteins, most fluorescent readouts require that labeling is strictly limited to the protein of interest located at the cell surface. While such data have so far been missing in the literature, they suggest that for applications where labeling of unwanted molecules would affect the conclusions, researchers need to be aware of this potential non-specificity of PPTase methods when selecting a labeling strategy. We show, again by quantitative comparison, that the HaloTag is a viable alternative.
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Affiliation(s)
- Jakob C. Stüber
- Department of Biochemistry, University of Zurich, Winterthurerstrasse, Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse, Zurich, Switzerland
- * E-mail:
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14
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Yano Y, Matsuzaki K. Live-cell imaging of membrane proteins by a coiled-coil labeling method-Principles and applications. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:1011-1017. [PMID: 30831076 DOI: 10.1016/j.bbamem.2019.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/18/2019] [Accepted: 02/27/2019] [Indexed: 02/09/2023]
Abstract
In situ investigations in living cell membranes are important to elucidate the dynamic behaviors of membrane proteins in complex biomembrane environments. Protein-specific labeling is a key technique for the detection of a target protein by fluorescence imaging. The use of post-translational labeling methods using a genetically encodable tag and synthetic probes targeting the tag offer a smaller label size, labeling with synthetic fluorophores, and precise control of the labeling ratio in multicolor labeling compared with conventional genetic fusions with fluorescent proteins. This review focuses on tag-probe labeling studies for live-cell analysis of membrane proteins based on heterodimeric peptide pairs that form coiled-coil structures. The robust and simple peptide-peptide interaction enables not only labeling of membrane proteins by noncovalent interactions, but also covalent crosslinking and acyl transfer reactions guided by coiled-coil assembly. A number of studies have demonstrated that membrane protein behaviors in live cells, such as internalization of receptors and the oligomeric states of various membrane proteins (G-protein-coupled receptors, epidermal growth factor receptors, influenza A M2 channel, and glycopholin A), can be precisely analyzed using coiled-coil labeling, indicating the potential of this labeling method in membrane protein research.
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Affiliation(s)
- Yoshiaki Yano
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan.
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15
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Zhang D, Liu R, Bao C, Zhang C, Yang L, Deng L, Bao B, Yang J, Chen X, Lin Q, Yang Y, Zhu L. Development of Acrylamide-Based Rapid and Multicolor Fluorogenic Probes for High Signal-to-Noise Live Cell Imaging. Bioconjug Chem 2019; 30:184-191. [PMID: 30566325 DOI: 10.1021/acs.bioconjchem.8b00827] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein covalent labeling is dramatically useful for studying protein function in living cells and organisms. In this field, the chemical tag technique combined with fluorogenic probes has emerged as a powerful tool. Herein, a series of TMP tag fluorogenic probes have been developed to span the green to full blue spectral range. These probes feature an acrylamide unit that acts as a linker group to conjugate the fluorophore and the ligand as well as a quencher and a covalent reaction group. After the probes bind to eDHFR:L28C, the acrylamide unit specifically reacts with the thiol group of the L28C residue beside the ligand binding pocket, achieving protein-specific labeling without any liberation of leaving groups. With these probes, multicolor and specific protein labeling with a fast reaction rate ( t1/2 = 33 s) and dramatic fluorescence enhancement (4000-fold) were obtained. Furthermore, no-wash protein labeling in both living cells and zebrafish was successfully achieved. We expect it may provide a general and highly effective chemical tool for the study of protein function in living cells and organisms.
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Affiliation(s)
- Dasheng Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Chemistry and Molecular Engineering , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Renmei Liu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Pharmacy , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Chunyan Bao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Chemistry and Molecular Engineering , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Chenxia Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Pharmacy , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Lipeng Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Chemistry and Molecular Engineering , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Lei Deng
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Pharmacy , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Bingkun Bao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Chemistry and Molecular Engineering , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Jing Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Pharmacy , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Pharmacy , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Qiuning Lin
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Chemistry and Molecular Engineering , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Pharmacy , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
| | - Linyong Zhu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China.,School of Chemistry and Molecular Engineering , East China University of Science and Technology , 130 Mei Long Road , Shanghai 200237 , China
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16
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Soldevila-Barreda JJ, Metzler-Nolte N. Intracellular Catalysis with Selected Metal Complexes and Metallic Nanoparticles: Advances toward the Development of Catalytic Metallodrugs. Chem Rev 2019; 119:829-869. [PMID: 30618246 DOI: 10.1021/acs.chemrev.8b00493] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Platinum-containing drugs (e.g., cisplatin) are among the most frequently used chemotherapeutic agents. Their tremendous success has spurred research and development of other metal-based drugs, with notable achievements. Generally, the vast majority of metal-based drug candidates in clinical and developmental stages are stoichiometric agents, i.e., each metal complex reacts only once with their biological target. Additionally, many of these metal complexes are involved in side reactions, which not only reduce the effective amount of the drug but may also cause toxicity. On a separate note, transition metal complexes and nanoparticles have a well-established history of being potent catalysts for selective molecular transformations, with examples such as the Mo- and Ru-based catalysts for metathesis reactions (Nobel Prize in 2005) or palladium catalysts for C-C bond forming reactions such as Heck, Negishi, or Suzuki reactions (Nobel Prize in 2010). Also, notably, no direct biological equivalent of these transformations exists in a biological environment such as bacteria or mammalian cells. It is, therefore, only logical that recent interest has focused on developing transition-metal based catalytic systems that are capable of performing transformations inside cells, with the aim of inducing medicinally relevant cellular changes. Because unlike in stoichiometric reactions, a catalytically active compound may turn over many substrate molecules, only very small amounts of such a catalytic metallodrug are required to achieve a desired pharmacologic effect, and therefore, toxicity and side reactions are reduced. Furthermore, performing catalytic reactions in biological systems also opens the door for new methodologies to study the behavior of biomolecules in their natural state, e.g., via in situ labeling or by increasing/depleting their concentration at will. There is, of course, an art to the choice of catalysts and reactions which have to be compatible with biological conditions, namely an aqueous, oxygen-containing environment. In this review, we aim to describe new developments that bring together the far-distant worlds of transition-metal based catalysis and metal-based drugs, in what is termed "catalytic metallodrugs". Here we will focus on transformations that have been performed on small biomolecules (such as shifting equilibria like in the NAD+/NADH or GSH/GSSG couples), on non-natural molecules such as dyes for imaging purposes, or on biomacromolecules such as proteins. Neither reactions involving release (e.g., CO) or transformation of small molecules (e.g., 1O2 production), degradation of biomolecules such as proteins, RNA or DNA nor light-induced medicinal chemistry (e.g., photodynamic therapy) are covered, even if metal complexes are centrally involved in those. In each section, we describe the (inorganic) chemistry involved, as well as selected examples of biological applications in the hope that this snapshot of a new but quickly developing field will indeed inspire novel research and unprecedented interactions across disciplinary boundaries.
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Affiliation(s)
- Joan Josep Soldevila-Barreda
- Inorganic Chemistry I-Bioinorganic Chemistry , Ruhr University Bochum , Universitätsstrasse 150 , 44780-D Bochum , Germany
| | - Nils Metzler-Nolte
- Inorganic Chemistry I-Bioinorganic Chemistry , Ruhr University Bochum , Universitätsstrasse 150 , 44780-D Bochum , Germany
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17
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Zegota MM, Wang T, Seidler C, Wah Ng DY, Kuan SL, Weil T. "Tag and Modify" Protein Conjugation with Dynamic Covalent Chemistry. Bioconjug Chem 2018; 29:2665-2670. [PMID: 29949347 DOI: 10.1021/acs.bioconjchem.8b00358] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The development of small protein tags that exhibit bioorthogonality, bond stability, and reversibility, as well as biocompatibility, holds great promise for applications in cellular environments enabling controlled drug delivery or for the construction of dynamic protein complexes in biological environments. Herein, we report the first application of dynamic covalent chemistry both for purification and for reversible assembly of protein conjugates using interactions of boronic acid with diols and salicylhydroxamates. Incorporation of the boronic acid (BA) tag was performed in a site-selective fashion by applying disulfide rebridging strategy. As an example, a model protein enzyme (lysozyme) was modified with the BA tag and purified using carbohydrate-based column chromatography. Subsequent dynamic covalent "click-like" bioconjugation with a salicylhydroxamate modified fluorescent dye (BODIPY FL) was accomplished while retaining its original enzymatic activity.
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Affiliation(s)
- Maksymilian Marek Zegota
- Max-Planck Institute for Polymer Research , Ackermannweg 10 , 55128 Mainz , Germany.,Institute of Inorganic Chemistry I , University of Ulm , Albert-Einstein-Allee 11 , 89081 Ulm , Germany
| | - Tao Wang
- Institute of Inorganic Chemistry I , University of Ulm , Albert-Einstein-Allee 11 , 89081 Ulm , Germany.,School of Materials Science and Engineering , Southwest Jiaotong University , 610031 Chengdu , P.R. China
| | - Christiane Seidler
- Max-Planck Institute for Polymer Research , Ackermannweg 10 , 55128 Mainz , Germany.,Institute of Inorganic Chemistry I , University of Ulm , Albert-Einstein-Allee 11 , 89081 Ulm , Germany
| | - David Yuen Wah Ng
- Max-Planck Institute for Polymer Research , Ackermannweg 10 , 55128 Mainz , Germany.,Institute of Inorganic Chemistry I , University of Ulm , Albert-Einstein-Allee 11 , 89081 Ulm , Germany
| | - Seah Ling Kuan
- Max-Planck Institute for Polymer Research , Ackermannweg 10 , 55128 Mainz , Germany.,Institute of Inorganic Chemistry I , University of Ulm , Albert-Einstein-Allee 11 , 89081 Ulm , Germany
| | - Tanja Weil
- Max-Planck Institute for Polymer Research , Ackermannweg 10 , 55128 Mainz , Germany.,Institute of Inorganic Chemistry I , University of Ulm , Albert-Einstein-Allee 11 , 89081 Ulm , Germany
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18
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Wu M, Shu J. Multimodal Molecular Imaging: Current Status and Future Directions. CONTRAST MEDIA & MOLECULAR IMAGING 2018; 2018:1382183. [PMID: 29967571 PMCID: PMC6008764 DOI: 10.1155/2018/1382183] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/11/2018] [Accepted: 05/10/2018] [Indexed: 12/12/2022]
Abstract
Molecular imaging has emerged at the end of the last century as an interdisciplinary method involving in vivo imaging and molecular biology aiming at identifying living biological processes at a cellular and molecular level in a noninvasive manner. It has a profound role in determining disease changes and facilitating drug research and development, thus creating new medical modalities to monitor human health. At present, a variety of different molecular imaging techniques have their advantages, disadvantages, and limitations. In order to overcome these shortcomings, researchers combine two or more detection techniques to create a new imaging mode, such as multimodal molecular imaging, to obtain a better result and more information regarding monitoring, diagnosis, and treatment. In this review, we first describe the classic molecular imaging technology and its key advantages, and then, we offer some of the latest multimodal molecular imaging modes. Finally, we summarize the great challenges, the future development, and the great potential in this field.
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Affiliation(s)
- Min Wu
- Department of Radiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Jian Shu
- Department of Radiology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
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19
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Labeling of Membrane Complexes for Electron Microscopy. Methods Mol Biol 2018. [PMID: 28755367 DOI: 10.1007/978-1-4939-7151-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Localization of specific subunits or domains of interest inside protein complexes can be challenging, especially for membrane machineries. The amphipatic nature of their subunits and their modular organization results in difficult genetic manipulation and instability upon purification. Here, we present different labeling approaches that have been demonstrated successful in the structural characterization of large membrane complexes.
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20
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Yano Y, Furukawa N, Ono S, Takeda Y, Matsuzaki K. Selective amine labeling of cell surface proteins guided by coiled-coil assembly. Biopolymers 2017; 106:484-90. [PMID: 26285787 DOI: 10.1002/bip.22715] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/30/2015] [Accepted: 08/09/2015] [Indexed: 01/17/2023]
Abstract
Covalent labeling of target proteins in living cells is useful for both fluorescence live-cell imaging and the subsequent biochemical analyses of the proteins. Here, we report an efficient method for the amine labeling of membrane proteins on the cell surface, guided by a noncovalent coiled-coil interaction. A carboxyl sulfosuccinimidyl ester introduced at the C-terminus of the coiled-coil probe reacted with target proteins under mild labeling conditions ([probe] = 150 nM, pH 7.4, 25°C) for 20 min. Various fluorescent moieties with different hydrophobicities are available for covalent labeling with high signal/background labeling ratios. Using this method, oligomeric states of glycophorin A (GpA) were compared in mammalian CHO-K1 cells and sodium dodecyl sulfate (SDS) micelles. In the cell membranes, no significant self-association of GpA was detected, whereas SDS-PAGE suggested partial dimerization of the proteins. Membrane cholesterol was found to be an important factor that suppressed the dimerization of GpA. Thus, the covalent functionality enables direct comparison of the oligomeric state of membrane proteins under various conditions. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 484-490, 2016.
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Affiliation(s)
- Yoshiaki Yano
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-Ku, Kyoto, 606-8501, Japan
| | - Nami Furukawa
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-Ku, Kyoto, 606-8501, Japan
| | - Satoshi Ono
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-Ku, Kyoto, 606-8501, Japan
| | - Yuki Takeda
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-Ku, Kyoto, 606-8501, Japan
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-Ku, Kyoto, 606-8501, Japan
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21
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In Vivo Analysis of Protein-Protein Interactions with Bioluminescence Resonance Energy Transfer (BRET): Progress and Prospects. Int J Mol Sci 2016; 17:ijms17101704. [PMID: 27727181 PMCID: PMC5085736 DOI: 10.3390/ijms17101704] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/26/2016] [Accepted: 09/29/2016] [Indexed: 11/17/2022] Open
Abstract
Proteins are the elementary machinery of life, and their functions are carried out mostly by molecular interactions. Among those interactions, protein-protein interactions (PPIs) are the most important as they participate in or mediate all essential biological processes. However, many common methods for PPI investigations are slightly unreliable and suffer from various limitations, especially in the studies of dynamic PPIs. To solve this problem, a method called Bioluminescence Resonance Energy Transfer (BRET) was developed about seventeen years ago. Since then, BRET has evolved into a whole class of methods that can be used to survey virtually any kinds of PPIs. Compared to many traditional methods, BRET is highly sensitive, reliable, easy to perform, and relatively inexpensive. However, most importantly, it can be done in vivo and allows the real-time monitoring of dynamic PPIs with the easily detectable light signal, which is extremely valuable for the PPI functional research. This review will take a comprehensive look at this powerful technique, including its principles, comparisons with other methods, experimental approaches, classifications, applications, early developments, recent progress, and prospects.
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22
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Pratt SE, Speltz EB, Mochrie SGJ, Regan L. Designed Proteins as Novel Imaging Reagents in Living Escherichia coli. Chembiochem 2016; 17:1652-7. [PMID: 27304706 DOI: 10.1002/cbic.201600252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Indexed: 11/06/2022]
Abstract
Fluorescence imaging is a powerful tool to study protein function in living cells. Here, we introduce a novel imaging strategy that is fully genetically encodable, does not require the use of exogenous substrates, and adds a minimally disruptive tag to the protein of interest (POI). Our method was based on a set of designed tetratricopeptide repeat affinity proteins (TRAPs) that specifically and reversibly interact with a short, extended peptide tag. We co-expressed the TRAPs fused to fluorescent proteins (FPs) and the peptide tags fused to the POIs. We illustrated the method using the Escherichia coli protein FtsZ and showed that our system could track distinct FtsZ structures under both low and high expression conditions in live cells. We anticipate that our imaging strategy will be a useful tool for imaging the subcellular localization of many proteins, especially those recalcitrant to imaging by direct tagging with FPs.
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Affiliation(s)
- Susan E Pratt
- Department of Physics, Yale University, 217 Prospect Street, New Haven, CT, 06511, USA.,Integrated Graduate Program in Physical and Engineering Biology, Yale University, 266 Whitney Avenue, New Haven, CT, 06511, USA
| | - Elizabeth B Speltz
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT, 06511, USA
| | - Simon G J Mochrie
- Department of Physics, Yale University, 217 Prospect Street, New Haven, CT, 06511, USA. .,Integrated Graduate Program in Physical and Engineering Biology, Yale University, 266 Whitney Avenue, New Haven, CT, 06511, USA. .,Department of Applied Physics, Yale University, 15 Prospect Street, New Haven, CT, 06511, USA.
| | - Lynne Regan
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, 266 Whitney Avenue, New Haven, CT, 06511, USA. .,Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT, 06511, USA. .,Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT, 06511, USA.
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23
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Nakase I. [Creation of artificial receptors activated by coiled-coil peptides and cellular regulation]. YAKUGAKU ZASSHI 2016; 135:375-81. [PMID: 25759046 DOI: 10.1248/yakushi.14-00240-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Exploiting the ability of coiled-coil peptides to induce dimer formation, we designed an artificial epidermal growth factor receptor (EGFR) in which dimerization is essential for increasing the tyrosine kinase activity of its intracellular domain. Using leucine-zipper coiled-coil peptides, the surface-exposed E3 ((EIAALEK)3) tag sequence was fused with EGFR (E3-EGFR) lacking domains I-III and a part of IV, which participate in dimerization of EGFR after binding to natural ligand (that is, epidermal growth factor). To dimerize E3-EGFR we synthesized conjugates of two K4 ((KIAALKE)4) peptides, called K4-conjugates, with linker lengths approximately 10 angstrom that mimic the distance of EGFR dimerization. Receptor phosphorylation of E3-EGFR was found to increase within 5 min in CHO cells expressing E3-EGFR after treatment with K4 conjugates. Increased lamellipodia formation and migration of the cells was also observed when treated with the artificial ligands. This receptor model can be applied to a wide variety of membrane-associated proteins to control cellular processes and to elucidate the functional mechanisms of these proteins using chemical biology.
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Affiliation(s)
- Ikuhiko Nakase
- Nanoscience and Nanotechnology Research Center, Research Organization for the 21st Century, Osaka Prefecture University
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24
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Choi S, Kim H, Kim SY, Yang EG. Probing protein complexes inside living cells using a silicon nanowire-based pull-down assay. NANOSCALE 2016; 8:11380-11384. [PMID: 27198202 DOI: 10.1039/c6nr00171h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Most proteins perform their functions as interacting complexes. Here we propose a novel method for capturing an intracellular protein and its interacting partner out of living cells by utilizing intracellular access of antibody modified vertical silicon nanowire arrays whose surface is covered with a polyethylene glycol layer to prevent strong cell adhesion. Such a feature facilitates the removal of cells by simple washing, enabling subsequent detection of a pulled-down protein and its interacting partner, and further assessment of a drug-induced change in the interacting complex. Our new SiNW-based tool is thus suitable for authentication of protein networks inside living cells.
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Affiliation(s)
- Sojoong Choi
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea.
| | - Hyunju Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea.
| | - So Yeon Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea. and Department of Biomedical Engineering, Korea University of Science and Technology (UST), KIST campus, Seoul 02792, Republic of Korea
| | - Eun Gyeong Yang
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea. and Department of Biological Chemistry, Korea University of Science and Technology (UST), KIST campus, Seoul 02792, Republic of Korea
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25
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Meyer SA, Ozbay BN, Potcoava M, Salcedo E, Restrepo D, Gibson EA. Super-resolution imaging of ciliary microdomains in isolated olfactory sensory neurons using a custom two-color stimulated emission depletion microscope. JOURNAL OF BIOMEDICAL OPTICS 2016; 21:66017. [PMID: 27367253 PMCID: PMC4923803 DOI: 10.1117/1.jbo.21.6.066017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 06/03/2016] [Indexed: 06/06/2023]
Abstract
We performed stimulated emission depletion (STED) imaging of isolated olfactory sensory neurons (OSNs) using a custom-built microscope. The STED microscope uses a single pulsed laser to excite two separate fluorophores, Atto 590 and Atto 647N. A gated timing circuit combined with temporal interleaving of the different color excitation/STED laser pulses filters the two channel detection and greatly minimizes crosstalk. We quantified the instrument resolution to be ∼81 and ∼44 nm, for the Atto 590 and Atto 647N channels. The spatial separation between the two channels was measured to be under 10 nm, well below the resolution limit. The custom-STED microscope is incorporated onto a commercial research microscope allowing brightfield, differential interference contrast, and epifluorescence imaging on the same field of view. We performed immunolabeling of OSNs in mice to image localization of ciliary membrane proteins involved in olfactory transduction. We imaged Ca2+-permeable cyclic nucleotide gated (CNG) channel (Atto 594) and adenylyl cyclase type III (ACIII) (Atto 647N) in distinct cilia. STED imaging resolved well-separated subdiffraction limited clusters for each protein. We quantified the size of each cluster to have a mean value of 88±48 nm and 124±43 nm, for CNG and ACIII, respectively. STED imaging showed separated clusters that were not resolvable in confocal images.
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Affiliation(s)
- Stephanie A. Meyer
- University of Colorado Denver Anschutz Medical Campus, Department of Bioengineering, MS 8607, 12700 East 19th Avenue, Aurora, Colorado 80045-2560, United States
| | - Baris N. Ozbay
- University of Colorado Denver Anschutz Medical Campus, Department of Bioengineering, MS 8607, 12700 East 19th Avenue, Aurora, Colorado 80045-2560, United States
| | - Mariana Potcoava
- University of Colorado Denver Anschutz Medical Campus, Department of Bioengineering, MS 8607, 12700 East 19th Avenue, Aurora, Colorado 80045-2560, United States
| | - Ernesto Salcedo
- University of Colorado Denver Anschutz Medical Campus, Department of Cell and Developmental Biology, MS 8108, 12801 East 17th Avenue, Aurora, Colorado 80045-2560, United States
| | - Diego Restrepo
- University of Colorado Denver Anschutz Medical Campus, Department of Cell and Developmental Biology, MS 8108, 12801 East 17th Avenue, Aurora, Colorado 80045-2560, United States
| | - Emily A. Gibson
- University of Colorado Denver Anschutz Medical Campus, Department of Bioengineering, MS 8607, 12700 East 19th Avenue, Aurora, Colorado 80045-2560, United States
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Etemadzadeh MH, Arashkia A, Roohvand F, Norouzian D, Azadmanesh K. Isolation, cloning, and expression of E. coli BirA gene for biotinylation applications. Adv Biomed Res 2015; 4:149. [PMID: 26380234 PMCID: PMC4551058 DOI: 10.4103/2277-9175.161576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 03/12/2014] [Indexed: 11/16/2022] Open
Abstract
Background: The key enzyme in biotin-(strept) avidin systems, Escherichia coli BirA biotin ligase, is currently obtained by overexpression of the long protein-tagged versions of the gene to prevent its toxic effect in E. coli. Herein we describe a rather simple and efficient system for expression of E. coli BirA without the application of long-tag proteins. Materials and Methods: The coding sequence of BirA gene was isolated by polymerase chain reaction using DNA extract of E. coli-DH5α as template. BirA amplicon harboring a GS-linker at its C-terminal was cloned into NdeI-XhoI sites of pET24a(+) vector under control of T7 promoter and upstream of the vector-derived 6xHis-tag. pET24-BirA transformed BL21-cells were induced for protein expression by IPTG and analyzed by SDS-PAGE and Western blotting. Protein expression yields were assessed by image analysis of the SDS-PAGE scans using ImageJ software. Result: Agarose gel electrophoresis indicated proper size of the BirA gene amplicon (963 bp) and accuracy of the recombinant pET24-BirA construct. Sequence alignment analysis indicated identical sequence (100%) of our isolate with that of the standard E. coli-K12 BirA gene sequence (accession number: NC_000913.3). SDS-PAGE and Western blot results indicated specific expression of the 36.6 kDa protein corresponding to the BirA protein. Image analysis estimated a yield of 12% of total protein for the BirA expression. Conclusions: By application of pET24a(+) we achieved relatively high expression of BirA in E. coli without application of any long protein-tags. Introduction of the present expression system may provide more readily available source of BirA enzyme for (strept) avidin–biotin applications and studies.
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Affiliation(s)
| | - Arash Arashkia
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Farzin Roohvand
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Dariush Norouzian
- Department of Pilot Biotechnology, Pasteur Institute of Iran, Tehran, Iran
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27
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Measuring receptor recycling in polarized MDCK cells. Methods Cell Biol 2015. [PMID: 26360039 DOI: 10.1016/bs.mcb.2015.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Recycling of proteins such as channels, pumps, and receptors is critical for epithelial cell function. In this chapter we present a method to measure receptor recycling in polarized Madin-Darby canine kidney cells using an iodinated ligand. We describe a technique to iodinate transferrin (Tf), we discuss how (125)I-Tf can be used to label a cohort of endocytosed Tf receptor, and then we provide methods to measure the rate of recycling of the (125)I-Tf-receptor complex. We also show how this approach, which is easily adaptable to other proteins, can be used to simultaneously measure the normally small amount of (125)I-Tf transcytosis and degradation.
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Mu J, Liu F, Rajab MS, Shi M, Li S, Goh C, Lu L, Xu QH, Liu B, Ng LG, Xing B. A Small-Molecule FRET Reporter for the Real-Time Visualization of Cell-Surface Proteolytic Enzyme Functions. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407182] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Mu J, Liu F, Rajab MS, Shi M, Li S, Goh C, Lu L, Xu QH, Liu B, Ng LG, Xing B. A Small-Molecule FRET Reporter for the Real-Time Visualization of Cell-Surface Proteolytic Enzyme Functions. Angew Chem Int Ed Engl 2014; 53:14357-62. [DOI: 10.1002/anie.201407182] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/26/2014] [Indexed: 01/16/2023]
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30
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In vivo single-molecule imaging identifies altered dynamics of calcium channels in dystrophin-mutant C. elegans. Nat Commun 2014; 5:4974. [PMID: 25232639 PMCID: PMC4199201 DOI: 10.1038/ncomms5974] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 08/12/2014] [Indexed: 01/15/2023] Open
Abstract
Single-molecule (SM) fluorescence microscopy allows the imaging of biomolecules in cultured cells with a precision of a few nanometres but has yet to be implemented in living adult animals. Here we used split-GFP (green fluorescent protein) fusions and complementation-activated light microscopy (CALM) for subresolution imaging of individual membrane proteins in live Caenorhabditis elegans (C. elegans). In vivo tissue-specific SM tracking of transmembrane CD4 and voltage-dependent Ca2+ channels (VDCC) was achieved with a precision of 30 nm within neuromuscular synapses and at the surface of muscle cells in normal and dystrophin-mutant worms. Through diffusion analyses, we reveal that dystrophin is involved in modulating the confinement of VDCC within sarcolemmal membrane nanodomains in response to varying tonus of C. elegans body-wall muscles. CALM expands the applications of SM imaging techniques beyond the petri dish and opens the possibility to explore the molecular basis of homeostatic and pathological cellular processes with subresolution precision, directly in live animals. Single molecule fluorescence microscopy is a powerful technique to study protein dynamics in cells, but it has not been applied to adult animals. The authors use complementation-activated light microscopy in C. elegansto discover that dystrophin regulates the diffusion properties of voltage-dependent calcium ion channels at the surface of body-wall muscle cells.![]()
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31
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Kawano K. [Stoichiometric analysis of oligomerization of membrane proteins using coiled-coil labeling and in-cell spectroscopy]. YAKUGAKU ZASSHI 2014; 134:931-7. [PMID: 25174363 DOI: 10.1248/yakushi.14-00162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Many membrane proteins are responsible for signaling and ionic transport necessary to maintain biological functions in vivo. Recently, not only conformational changes but also oligomerization have been proposed to regulate protein activation. Thus, the study of membrane protein oligomerization is crucial for new drug development. The existing destructive methodologies such as immunoprecipitation, however, are not suitable to determine oligomeric states precisely because of the artificial aggregation of proteins after detergent solubilization. In the present study, the coiled-coil tag-probe labeling method and spectral imaging were first combined to establish a new methodology based on fluorescence resonance energy transfer (FRET) for stoichiometric analysis of the oligomeric states of membrane proteins on living cells. After validating the method for mono-, di-, and tetrameric standard membrane proteins, the oligomeric state of β₂-adrenergic receptors (β₂ARs) was examined to clarify its functional significance. It was found that β2ARs could transduce cyclic adenosine 5'-monophosphate (cAMP) signals and internalize them upon treatment with ligands without showing any FRET signals. Thus, β₂ARs do not form constitutive homooligomers, and homooligomerization is not necessary for the receptor function of β₂ARs. Finally, the oligomeric state of full-length M2 proton-selective channels of influenza A virus was investigated. Although the results of X-ray crystallography and NMR studies using fragment peptides suggested that M2 stably forms a tetrameric channel, the full-length M2 proteins formed proton-conducting dimers at neutral pH and these dimers were converted to tetramers at acidic pH, indicating that the minimal functional unit of the M2 channel is a dimer.
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Affiliation(s)
- Kenichi Kawano
- Department of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University
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32
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Yano Y, Kawano K, Omae K, Takeda Y, Matsuzaki S, Matsuzaki K. [A visualization tool for oligomerization and internalization of membrane proteins in living cells: coiled-coil labeling method]. YAKUGAKU ZASSHI 2014; 134:501-6. [PMID: 24694810 DOI: 10.1248/yakushi.13-00251-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genetic fusion of fluorescent/luminescent proteins to a target protein for specific labeling in living cells has been widely used to investigate the intracellular trafficking and oligomerization of the proteins. However, several limitations of fluorescent/luminescent proteins, such as considerable size, difficulty in controlling labeling ratio in multicolor labeling, can obscure true behaviors of the target proteins. To overcome these difficulties, post-translational labeling methods using pairs of small genetically-encodable 'tags' and synthetic 'probes' targeting the tags have been widely studied in recent years. We have developed a quick tag-probe labeling method using a high-affinity heterodimeric coiled-coil formation between the E3 tag (EIAALEK)3 attached to the target protein and the K4 probe (KIAALKE)4 labeled with a fluorophore. The labeling is cell-surface-specific and completed within 1 min, therefore suitable for monitoring oligomerization/internalization of membrane proteins on living cell surface. Taking advantage of easiness in multicolor labeling, we show that the oligomeric state of membrane proteins can be precisely analyzed based on fluorescence resonance energy transfer. By using this method, we found that β2 adrenergic receptors do not form constitutive homooligomers, and homooligomerization is not necessary for the receptor function. Furthermore, the degree of internalization of the β2 receptors following agonist stimulation was evaluated by ratiometric detection of pH decrease in endosomes.
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Affiliation(s)
- Yoshiaki Yano
- Department of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University
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33
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Feinstein TN. Cell-surface protein-protein interaction analysis with time-resolved FRET and snap-tag technologies. Methods Mol Biol 2014; 1066:121-9. [PMID: 23955739 DOI: 10.1007/978-1-62703-604-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Förster resonance energy transfer (FRET) is a proximity-dependent quantum effect that allows the measurement of protein interactions and conformational changes which are invisible to traditional forms of fluorescence or electron microscopy. However, FRET experiments often have difficulty detecting interactions that are transient and localized or occur in low abundance against a large background. This protocol describes a method of improving on the sensitivity and quantifiability of FRET experiments by using time-specific detection to isolate FRET-mediated acceptor emission from cross-talk excitation and all other sources of nonspecific fluorescence background.
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Affiliation(s)
- Timothy N Feinstein
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
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34
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Zope HR, Versluis F, Ordas A, Voskuhl J, Spaink HP, Kros A. In Vitro and In Vivo Supramolecular Modification of Biomembranes Using a Lipidated Coiled-Coil Motif. Angew Chem Int Ed Engl 2013; 52:14247-51. [DOI: 10.1002/anie.201306033] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 08/30/2013] [Indexed: 01/22/2023]
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35
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Zope HR, Versluis F, Ordas A, Voskuhl J, Spaink HP, Kros A. Supramolekulare In-vitro- und In-vivo-Funktionalisierung von Biomembranen durch ein lipidiertes Coiled-Coil-Bindungsmotiv. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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36
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Hori Y, Norinobu T, Sato M, Arita K, Shirakawa M, Kikuchi K. Development of Fluorogenic Probes for Quick No-Wash Live-Cell Imaging of Intracellular Proteins. J Am Chem Soc 2013; 135:12360-5. [DOI: 10.1021/ja405745v] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | | | | | - Kyohei Arita
- Graduate School of Medical Life
Science, Yokohama City University, Yokohama,
Kanagawa 230-0045, Japan
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37
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Kawano K, Yano Y, Omae K, Matsuzaki S, Matsuzaki K. Stoichiometric analysis of oligomerization of membrane proteins on living cells using coiled-coil labeling and spectral imaging. Anal Chem 2013; 85:3454-61. [PMID: 23427815 DOI: 10.1021/ac400177a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Many membrane proteins are proposed to work as oligomers; however, the conclusion is sometimes controversial, as for β2-adorenergic receptor (β2AR), which is one of the best-studied family A G-protein-coupled receptors. This is due to the lack of methods for easy and precise detection of the oligomeric state of membrane proteins on living cells. Here, we show that a combination of the coiled-coil tag-probe labeling method and spectral imaging enable a stoichiometric analysis of the oligomeric state of membrane proteins on living cells using monomeric, dimeric, and tetrameric standard membrane proteins. Using this method, we found that β2ARs do not form constitutive homooligomers, while they exhibit their functions such as the cyclic adenosine 5'-monophosphate (cAMP) signaling and internalization upon agonist stimulation.
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Affiliation(s)
- Kenichi Kawano
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
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38
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Otterstrom J, van Oijen AM. Visualization of membrane fusion, one particle at a time. Biochemistry 2013; 52:1654-68. [PMID: 23421412 DOI: 10.1021/bi301573w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein-mediated fusion between phospholipid bilayers is a fundamental and necessary mechanism for many cellular processes. The short-lived nature of the intermediate states visited during fusion makes it challenging to capture precise kinetic information using classical, ensemble-averaging biophysical techniques. Recently, a number of single-particle fluorescence microscopy-based assays that allow researchers to obtain highly quantitative data about the fusion process by observing individual fusion events in real time have been developed. These assays depend upon changes in the acquired fluorescence signal to provide a direct readout for transitions between the various fusion intermediates. The resulting data yield meaningful and detailed kinetic information about the transitory states en route to productive membrane fusion. In this review, we highlight recent in vitro and in vivo studies of membrane fusion at the single-particle level in the contexts of viral membrane fusion and SNARE-mediated synaptic vesicle fusion. These studies afford insight into mechanisms of coordination between fusion-mediating proteins as well as coordination of the overall fusion process with other cellular processes. The development of single-particle approaches to investigate membrane fusion and their successful application to a number of model systems have resulted in a new experimental paradigm and open up considerable opportunities to extend these methods to other biological processes that involve membrane fusion.
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Affiliation(s)
- Jason Otterstrom
- Harvard Biophysics Program, Harvard Medical School , 240 Longwood Avenue, Boston, Massachusetts 02115, United States
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39
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Ono S, Yano Y, Matsuzaki K. Improvement of probe peptides for coiled-coil labeling by introducing phosphoserines. Biopolymers 2012; 98:234-8. [PMID: 22782565 DOI: 10.1002/bip.22059] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We have developed a method of rapidly labeling membrane proteins in living cells using a high-affinity heterodimeric coiled-coil construct containing an E3 tag (EIAALEK)(3) genetically fused to the target protein and a K4 probe (KIAALKE)(4) labeled with a fluorophore such as tetramethylrhodamine (TMR) at its N-terminus (TMR-K4). However, coiled-coil labeling cannot be applied to highly negatively charged cell lines such as HEK293, because of the nonspecific adsorption of the positively charged K4 probes to cell membranes. To reduce the net positive charge, we synthesized new probes that include phosphoserine residues (pSer) between the K4 sequence and TMR fluorophore (TMR-(pSer)(n)-K4, [n = 1-3]). The affinity of the pSer-introduced probes was comparable to that of the TMR-K4 probe. However, the TMR-(pSer)(2)-K4 and TMR-(pSer)(3)-K4 probes tended to aggregate during labeling. In contrast, TMR-pSer-K4, which was as soluble as TMR-K4, achieved higher signal/background ratios (30-100) for four host cell lines (HEK293, HeLa, SH-SY5Y, and PC12) than did TMR-K4 (~10 for HEK293 cells), demonstrating that the improved probe can be used for various types of cells.
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Affiliation(s)
- Satoshi Ono
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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40
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James ML, Gambhir SS. A molecular imaging primer: modalities, imaging agents, and applications. Physiol Rev 2012; 92:897-965. [PMID: 22535898 DOI: 10.1152/physrev.00049.2010] [Citation(s) in RCA: 702] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Molecular imaging is revolutionizing the way we study the inner workings of the human body, diagnose diseases, approach drug design, and assess therapies. The field as a whole is making possible the visualization of complex biochemical processes involved in normal physiology and disease states, in real time, in living cells, tissues, and intact subjects. In this review, we focus specifically on molecular imaging of intact living subjects. We provide a basic primer for those who are new to molecular imaging, and a resource for those involved in the field. We begin by describing classical molecular imaging techniques together with their key strengths and limitations, after which we introduce some of the latest emerging imaging modalities. We provide an overview of the main classes of molecular imaging agents (i.e., small molecules, peptides, aptamers, engineered proteins, and nanoparticles) and cite examples of how molecular imaging is being applied in oncology, neuroscience, cardiology, gene therapy, cell tracking, and theranostics (therapy combined with diagnostics). A step-by-step guide to answering biological and/or clinical questions using the tools of molecular imaging is also provided. We conclude by discussing the grand challenges of the field, its future directions, and enormous potential for further impacting how we approach research and medicine.
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Affiliation(s)
- Michelle L James
- Molecular Imaging Program, Department of Radiology, Stanford University, Palo Alto, CA 94305, USA
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41
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Nakase I, Okumura S, Tanaka G, Osaki K, Imanishi M, Futaki S. Signal Transduction Using an Artificial Receptor System that Undergoes Dimerization Upon Addition of a Bivalent Leucine-Zipper Ligand. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201805] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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42
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Nakase I, Okumura S, Tanaka G, Osaki K, Imanishi M, Futaki S. Signal transduction using an artificial receptor system that undergoes dimerization upon addition of a bivalent leucine-zipper ligand. Angew Chem Int Ed Engl 2012; 51:7464-7. [PMID: 22711581 DOI: 10.1002/anie.201201805] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Indexed: 01/20/2023]
Affiliation(s)
- Ikuhiko Nakase
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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43
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Hori Y, Nakaki K, Sato M, Mizukami S, Kikuchi K. Development of Protein-Labeling Probes with a Redesigned Fluorogenic Switch Based on Intramolecular Association for No-Wash Live-Cell Imaging. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200867] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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44
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Hori Y, Nakaki K, Sato M, Mizukami S, Kikuchi K. Development of Protein-Labeling Probes with a Redesigned Fluorogenic Switch Based on Intramolecular Association for No-Wash Live-Cell Imaging. Angew Chem Int Ed Engl 2012; 51:5611-4. [DOI: 10.1002/anie.201200867] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 03/19/2012] [Indexed: 01/28/2023]
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45
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Sueda S, Tanaka S, Inoue S, Komatsu H. A luminescent affinity tag for proteins based on the terbium(III)-binding peptide. Anal Biochem 2012; 422:52-4. [DOI: 10.1016/j.ab.2011.12.050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Revised: 12/29/2011] [Accepted: 12/29/2011] [Indexed: 11/25/2022]
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46
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Takeda Y, Yano Y, Matsuzaki K. High-throughput analysis of ligand-induced internalization of β2-adrenoceptors using the coiled-coil tag-probe method. Anal Chem 2012; 84:1754-9. [PMID: 22243418 DOI: 10.1021/ac203231n] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Receptor internalization is a useful indicator of the activity of ligands. The N-terminus of the β(2)-adrenergic receptor expressed on the cell surface was labeled with fluorophores using a novel coiled-coil labeling system. Endocytosis of the receptors was automatically detected using a fluorescence image analyzer by evaluating (1) translocation of the receptor from cell-surface to intracellular regions and (2) acidification in endosomes. Both parameters increased upon agonist stimulation in a dose-dependent manner. The extent of endocytosis was significantly dependent on the agonist used, indicating the presence of a biased signaling for endocytosis. The receptor antagonists can also be screened by competitive inhibition of agonist-induced endocytosis. The image analysis approach has proven to be useful for high-throughput characterization and screening of GPCR ligands.
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Affiliation(s)
- Yuki Takeda
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
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47
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Yano Y, Kawano K, Omae K, Matsuzaki K. Coiled-coil tag-probe labeling methods for live-cell imaging of membrane receptors. Methods Enzymol 2012; 504:355-70. [PMID: 22264544 DOI: 10.1016/b978-0-12-391857-4.00018-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Tag-probe labeling methods have advantages over conventional fusion with fluorescent proteins in terms of smaller labels, surface specificity, availability of pulse labeling, and ease of multicolor labeling. With this method, the gene of the target protein is fused with a short tag sequence, expressed in cells, and the protein is labeled with exogenous fluorescent probes that specifically bind to the tag. Various labeling principles, such as protein-ligand interaction, peptide-peptide interaction, peptide-metal interaction, and enzymatic reactions, have been applied to the tag-probe labeling of membrane receptors. We describe our coiled-coil tag-probe method in detail, including the design and synthesis of the tag and probe, labeling procedures, and observations by confocal microscopy. Applications to the analysis of receptor internalization and oligomerization are also introduced.
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Affiliation(s)
- Yoshiaki Yano
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
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48
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Yano Y, Matsuzaki K. Fluorescence ratiometric detection of ligand-induced receptor internalization using extracellular coiled-coil tag-probe labeling. FEBS Lett 2011; 585:2385-8. [PMID: 21708150 DOI: 10.1016/j.febslet.2011.06.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 06/10/2011] [Indexed: 10/18/2022]
Abstract
We report a new method for the detection of ligand-induced receptor internalization by fluorescence ratiometric imaging of pH in endosomes in combination with a recently developed posttranslational labeling system based on the formation of a heterodimeric coiled-coil structure. The N-terminus of the β2-adrenergic receptor expressed on the cell surface was doubly labeled with pH-sensitive fluorescein and pH-insensitive tetramethylrhodamine. A significant increase in the tetramethylrhodamine-to-fluorescein fluorescence intensity ratio was observed after incubation with agonists in a concentration-dependent manner. This simple and accurate method of detecting the agonistic activity of receptors will be useful for high-throughput screening of drug candidates.
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Affiliation(s)
- Yoshiaki Yano
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
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49
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Sueda S, Yoneda S, Hayashi H. Site-Specific Labeling of Proteins by Using Biotin Protein Ligase Conjugated with Fluorophores. Chembiochem 2011; 12:1367-75. [DOI: 10.1002/cbic.201000738] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Indexed: 01/30/2023]
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50
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Targeting and imaging single biomolecules in living cells by complementation-activated light microscopy with split-fluorescent proteins. Proc Natl Acad Sci U S A 2011; 108:E201-10. [PMID: 21606345 DOI: 10.1073/pnas.1101929108] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-molecule (SM) microscopy allows outstanding insight into biomolecular mechanisms in cells. However, selective detection of single biomolecules in their native environment remains particularly challenging. Here, we introduce an easy methodology that combines specific targeting and nanometer accuracy imaging of individual biomolecules in living cells. In this method, named complementation-activated light microscopy (CALM), proteins are fused to dark split-fluorescent proteins (split-FPs), which are activated into bright FPs by complementation with synthetic peptides. Using CALM, the diffusion dynamics of a controlled subset of extracellular and intracellular proteins are imaged with nanometer precision, and SM tracking can additionally be performed with fluorophores and quantum dots. In cells, site-specific labeling of these probes is verified by coincidence SM detection with the complemented split-FP fusion proteins or intramolecular single-pair Förster resonance energy transfer. CALM is simple and combines advantages from genetically encoded and synthetic fluorescent probes to allow high-accuracy imaging of single biomolecules in living cells, independently of their expression level and at very high probe concentrations.
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